mix,api,resources: Start making the plot system more flexible

R/api.R

@@ -491,9 +491,57 @@ subset_summary <- function(m) {
     m
 }
 
-
 #' @export
 create_plots <- function(m) {
+    ## Empty ms1_plot table.
+    
+
+    ## Select the data nedeed for plotting.
+    x <- m$out$tab$flt_summ
+    ms1_plot_data <- gen_base_ms1_plot_tab(summ=x,
+                                           ms1_spec=m$out$tab$ms1_spec)
+
+    group_data <- m$conf$figures$grouping
+    plot_group <- group_data$group
+    plot_plot <- group_data$plot
+    plot_label <- group_data$label
+    plot_index <- c(plot_group,plot_plot,plot_label)
+
+    ## All the possible curve labels.
+    all_labels <- x[,unique(.SD),.SDcols=plot_label][[plot_label]]
+    
+    ## Plot styling.
+    style_eic_ms1 <- plot_decor(m,m$conf$logaxes$ms1_eic_int,
+                                all_labels=all_labels,
+                                legend_name=plot_label)
+    style_eic_ms2 <- plot_decor(m,m$conf$logaxes$ms2_eic_int,
+                                all_labels=all_labels,
+                                legend_name=plot_label)
+    style_spec_ms2 <- plot_decor(m,m$conf$logaxes$ms2_spec_int,
+                                 all_labels=all_labels,
+                                 legend_name = plot_label)
+
+    ## Generate MS1 EIC plots.
+    ms1_plot <- ms1_plot_data[,.(fig={
+        df <- .SD[,data.table::rbindlist(Map(function (a,b,c,d) {
+            s <- a[[1]]
+            s$plot_label <- b
+            s$rt_peak <- c
+            s$mz <- d
+            s},
+            eicMS1,
+            .SD[[..plot_label]],
+            rt_peak,
+            mz))]
+        list(plot_eic_ms1(df,style_fun = style_eic_ms1,
+                          plot_label = ..plot_label))
+        
+    }),by=c(plot_group,plot_plot)]
+    m$out$tab$ms1_plot <- ms1_plot
+    m
+}
+
+create_plots_old <- function(m) {
     ## Helpers
     textf <- ggplot2::element_text
     x <- m$out$tab$ms1_spec

R/mix.R

@@ -1045,3 +1045,70 @@ get_coord_lim <- function(new,def) {
     if (length(new[[2]])==0) res[[2]]<-def[[2]]
     res
 }
+
+
+
+gen_base_ms1_plot_tab <- function(summ,ms1_spec) {
+    
+    ident <- c("set",
+               "adduct",
+               "tag",
+               "ID",
+               "mz",
+               "Files")
+    
+    res <- summ[ms1_spec,c(.SD,
+                           list(rt_peak=i.ms1_rt,
+                                eicMS1=lapply(i.eicMS1,list))),
+                           .SDcols=ident,
+                           on=BASE_KEY,
+                nomatch=NULL]
+    setkeyv(res,cols=BASE_KEY)
+    res
+}
+plot_decor <- function(m,islog,all_labels,legend_name) {
+    textf <- ggplot2::element_text
+
+    ## Logarithmic, or linear y axis?
+    scale_y <- if (shiny::isTruthy(islog))
+                       ggplot2::scale_y_log10 else ggplot2::scale_y_continuous
+
+    rt_new_lim <- c(rt_in_min(m$conf$figures$rt_min),
+                    rt_in_min(m$conf$figures$rt_max))
+    rt_lim <- get_coord_lim(rt_new_lim,DEFAULT_RT_RANGE)
+
+    my_theme <- function (...) ggplot2::theme()
+
+    getpal <- colorRampPalette(RColorBrewer::brewer.pal(8,"Dark2"))
+    
+    col_all_vals <- getpal(length(all_labels))
+    names(col_all_vals) <- all_labels
+    scale_colour <- function(breaks, labels, ...) ggplot2::scale_colour_manual(values = col_all_vals,
+                                                                               breaks = breaks,
+                                                                               labels = labels,
+                                                                               name = legend_name,...)
+    
+    my_coord <- ggplot2::coord_cartesian(xlim = rt_lim)
+
+    function(plot,breaks,labels) plot + my_coord + scale_colour(breaks=breaks,
+                                                                labels=labels) + scale_y() + my_theme() 
+}
+
+
+plot_eic_ms1 <- function(df,style_fun,plot_label) {
+    mk_leg_lab<-function(tag,rt) {if (length(tag) > 0) paste(tag,"; rt= ",formatC(rt,format='f',digits=RT_DIGITS)," min",sep='') else character(0)}
+
+    mz <- df[,unique(mz)]
+    tbl <- df[,.(verb_labs=mk_leg_lab(plot_label,rt_peak),plot_label),
+              by=c("plot_label","rt_peak")]
+    verb_labs <- tbl[,verb_labs]
+    labs <- tbl[,plot_label]
+    df[,plot_label:=factor(plot_label)]
+    style_fun(ggplot2::ggplot(df,ggplot2::aes(x=rt,y=intensity,colour=plot_label)),
+              breaks=labs,
+              labels=verb_labs) +
+        ggplot2::geom_line(key_glyph=KEY_GLYPH) +
+        ggplot2::labs(x=CHR_GRAM_X,
+                      y=CHR_GRAM_Y)
+}
+

R/resources.R

@@ -174,7 +174,7 @@ QA_COLS <- c(QA_FLAGS,QA_NUM_REAL,QA_NUM_INT)
 MS2_SPEC_COLS <- c("adduct","ID","CE","rt","Files","spec","ms2_max_int")
 
 ## MS1 spectral table columns
-MS1_SPEC_COLS <- c("adduct","Files","ID","eicMS1","ms1_int","ms1_rt","ms1_mean")
+MS1_SPEC_COLS <- c("adduct","ID","eicMS1","ms1_int","ms1_rt","ms1_mean","Files")
 
 ## Default sorting keys of spectra in the summary table
 DEF_KEY_SUMM <- c("set","qa_pass","ms1_int","adduct","mz","tag")
@@ -193,3 +193,14 @@ FIG_DEF_SUBSET <- c("set","adduct","ID")
 
 REPORT_AUTHOR <- "Anonymous"
 REPORT_TITLE <- "Plots of EICs and MS2 Spectra"
+
+
+PLOT_FEATURES <- c("set",
+                   "adduct",
+                   "tag",
+                   "ID",
+                   "CE")
+
+## Select the most fundamental group of entries. Within this group,
+## each ID is unique.
+BASE_KEY <- c("adduct","Files","ID")